If your 'sit bones' are squarely on the saddle, and not at the very edges (if this is the case your saddle is to small,) you may be sliding forward so you end up with your weight resting on your taint. Tilt the saddle nose up quite a bit, and see if that helps.

Having a sizable cut out to keep your taint from being compressed is a good idea.
Excessive padding can also cause this, since as you sink into the foam, it compresses the soft tissue farther from your sit bones. Lots of padding feels great when you first use them, but on longish rides they kill.